Provided by: libbio-perl-perl_1.7.6-3_all

**NAME**

Bio::Matrix::PSM::SiteMatrix - SiteMatrixI implementation, holds a position scoring matrix (or position weight matrix) and log-odds

**SYNOPSIS**

use Bio::Matrix::PSM::SiteMatrix; # Create from memory by supplying probability matrix hash # both as strings or arrays # where the frequencies $a,$c,$g and $t are supplied either as # arrayref or string. Accordingly, lA, lC, lG and lT are the log # odds (only as arrays, no checks done right now) my ($a,$c,$g,$t,$score,$ic, $mid)=@_; #or my ($a,$c,$g,$t,$score,$ic,$mid)=('05a011','110550','400001', '100104',0.001,19.2,'CRE1'); #Where a stands for all (this frequency=1), see explanation below my %param=(-pA=>$a,-pC=>$c,-pG=>$g,-pT=>$t, -lA=>$la, -lC=>$lc,-lG=>$lg,-lT=>$l, -IC=>$ic,-e_val=>$score, -id=>$mid); my $site=Bio::Matrix::PSM::SiteMatrix->new(%param); #Or get it from a file: use Bio::Matrix::PSM::IO; my $psmIO= Bio::Matrix::PSM::IO->new(-file=>$file, -format=>'transfac'); while (my $psm=$psmIO->next_psm) { #Now we have a Bio::Matrix::PSM::Psm object, # see Bio::Matrix::PSM::PsmI for details #This is a Bio::Matrix::PSM::SiteMatrix object now my $matrix=$psm->matrix; } # Get a simple consensus, where alphabet is {A,C,G,T,N}, # choosing the character that both satisfies a supplied or default threshold # frequency and is the most frequenct character at each position, or N. # So for the position with A, C, G, T frequencies of 0.5, 0.25, 0.10, 0.15, # the simple consensus character will be 'A', whilst for 0.5, 0.5, 0, 0 it # would be 'N'. my $consensus=$site->consensus; # Get the IUPAC ambiguity code representation of the data in the matrix. # Because the frequencies may have been pseudo-count corrected, insignificant # frequences (below 0.05 by default) are ignored. So a position with # A, C, G, T frequencies of 0.5, 0.5, 0.01, 0.01 will get the IUPAC code 'M', # while 0.97, 0.01, 0.01, 0.01 will get the code 'A' and # 0.25, 0.25, 0.25, 0.25 would get 'N'. my $iupac=$site->IUPAC; # Getting/using regular expression (a representation of the IUPAC string) my $regexp=$site->regexp; my $count=grep($regexp,$seq); my $count=($seq=~ s/$regexp/$1/eg); print "Motif $mid is present $count times in this sequence\n";

**DESCRIPTION**

SiteMatrix is designed to provide some basic methods when working with position scoring (weight) matrices, such as transcription factor binding sites for example. A DNA PSM consists of four vectors with frequencies {A,C,G,T}. This is the minimum information you should provide to construct a PSM object. The vectors can be provided as strings with frequenciesx10 rounded to an int, going from {0..a} and 'a' represents the maximum (10). This is like MEME's compressed representation of a matrix and it is quite useful when working with relational DB. If arrays are provided as an input (references to arrays actually) they can be any number, real or integer (frequency or count). When creating the object you can ask the constructor to make a simple pseudo count correction by adding a number (typically 1) to all positions (with the -correction option). After adding the number the frequencies will be calculated. Only use correction when you supply counts, not frequencies. Throws an exception if: You mix as an input array and string (for example A matrix is given as array, C - as string). The position vector is (0,0,0,0). One of the probability vectors is shorter than the rest. Summary of the methods I use most frequently (details below): iupac - return IUPAC compliant consensus as a string score - Returns the score as a real number IC - information content. Returns a real number id - identifier. Returns a string accession - accession number. Returns a string next_pos - return the sequence probably for each letter, IUPAC symbol, IUPAC probability and simple sequence consenus letter for this position. Rewind at the end. Returns a hash. pos - current position get/set. Returns an integer. regexp - construct a regular expression based on IUPAC consensus. For example AGWV will be [Aa][Gg][AaTt][AaCcGg] width - site width get_string - gets the probability vector for a single base as a string. get_array - gets the probability vector for a single base as an array. get_logs_array - gets the log-odds vector for a single base as an array. New methods, which might be of interest to anyone who wants to store PSM in a relational database without creating an entry for each position is the ability to compress the PSM vector into a string with losing usually less than 1% of the data. this can be done with: my $str=$matrix->get_compressed_freq('A'); or my $str=$matrix->get_compressed_logs('A'); Loading from a database should be done with new, but is not yest implemented. However you can still uncompress such string with: my @arr=Bio::Matrix::PSM::_uncompress_string ($str,1,1); for PSM or my @arr=Bio::Matrix::PSM::_uncompress_string ($str,1000,2); for log odds

**FEEDBACK**

MailingListsUser feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to one of the Bioperl mailing lists. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/wiki/Mailing_lists - About the mailing listsSupportPlease direct usage questions or support issues to the mailing list:bioperl-l@bioperl.orgrather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.ReportingBugsReport bugs to the Bioperl bug tracking system to help us keep track the bugs and their resolution. Bug reports can be submitted via the web: https://github.com/bioperl/bioperl-live/issues

**AUTHOR** **-** **Stefan** **Kirov**

Email skirov@utk.edu

**CONTRIBUTORS**

Sendu Bala, bix@sendu.me.uk

**APPENDIX**

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _newTitle : new Usage : my $site=Bio::Matrix::PSM::SiteMatrix->new(-pA=>$a,-pC=>$c, -pG=>$g,-pT=>$t, -IC=>$ic, -e_val=>$score, -id=>$mid); Function: Creates a new Bio::Matrix::PSM::SiteMatrix object from memory Throws : If inconsistent data for all vectors (A,C,G and T) is provided, if you mix input types (string vs array) or if a position freq is 0. Returns : Bio::Matrix::PSM::SiteMatrix object Args : -pA => vector with the frequencies or counts of A -pC => vector for C -pG => vector for G -pt => vector for T -lA => vector for the log of A -lC => vector for the log of C -lG => vector for the log of G -lT => vector for the log of T -IC => real number, the information content of this matrix -e_val => real number, the expect value -id => string, an identifier -width => int, width of the matrix in nucleotides -sites => int, the number of sites that went into this matrix -model => hash ref, background frequencies for A, C, G and T -correction => number, the number to add to all positions to achieve pseudo count correction (default 0: no correction) NB: do not use correction when your input is frequences! -accession_number => string, an accession number Vectors can be strings of the frequencies where the frequencies are multiplied by 10 and rounded to the nearest whole number, and where 'a' is used to denote the maximal frequency 10. There should be no punctuation (spaces etc.) in the string. For example, 'a0501'. Alternatively frequencies or counts can be represented by an array ref containing the counts, frequencies or logs as any kind of number._calculate_consensusTitle : _calculate_consensus Function: Internal stuffcalc_weightTitle : calc_weight Usage : $obj->calc_weight({A=>0.2562, C=>0.2438, G=>0.2432, T=>0.2568}); Function: Recalculates the PSM (or weights) based on the PFM (the frequency matrix) and user supplied background model. Throws : if no model is supplied Returns : n/a Args : reference to a hash with background frequencies for A,C,G and Tnext_posTitle : next_pos Usage : Function: Retrieves the next position features: frequencies for A,C,G,T, the main letter (as in consensus) and the probabilty for this letter to occur at this position and the current position Returns : hash (pA,pC,pG,pT,logA,logC,logG,logT,base,prob,rel) Args : nonecurposTitle : curpos Usage : Function: Gets/sets the current position. Converts to 0 if argument is minus and to width if greater than width Returns : integer Args : integere_valTitle : e_val Usage : Function: Gets/sets the e-value Returns : real number Args : none to get, real number to setICTitle : IC Usage : Function: Get/set the Information Content Returns : real number Args : none to get, real number to setaccession_numberTitle : accession_number Function: Get/set the accession number, this will be unique id for the SiteMatrix object as well for any other object, inheriting from SiteMatrix Returns : string Args : none to get, string to setconsensusTitle : consensus Usage : Function: Returns the consensus Returns : string Args : (optional) threshold value 1 to 10, default 5 '5' means the returned characters had a 50% or higher presence at their positionwidthTitle : width Usage : Function: Returns the length of the sites in used to make this matrix Returns : int Args : nonesitesTitle : sites Usage : Function: Get/set the number of sites that were used to make this matrix Returns : int Args : none to get, int to setIUPACTitle : IUPAC Usage : Function: Returns IUPAC compliant consensus Returns : string Args : optionally, also supply a whole number (int) of 1 or higher to set the significance level when considering the frequencies. 1 (the default) means a 0.05 significance level: frequencies lower than 0.05 will be ignored. 2 Means a 0.005 level, and so on._to_IUPACTitle : _to_IUPAC Usage : Function: Converts a single position to IUPAC compliant symbol. For rules see the implementation Returns : char, real number Args : real numbers for frequencies of A,C,G,T (positional) optionally, also supply a whole number (int) of 1 or higher to set the significance level when considering the frequencies. 1 (the default) means a 0.05 significance level: frequencies lower than 0.05 will be ignored. 2 Means a 0.005 level, and so on._to_consTitle : _to_cons Usage : Function: Converts a single position to simple consensus character and returns its probability. For rules see the implementation Returns : char, real number Args : real numbers for A,C,G,T (positional), and optional 5th argument of threshold (as a number between 1 and 10, where 5 is default and means the returned character had a 50% or higher presence at this position)get_stringTitle : get_string Usage : Function: Returns given probability vector as a string. Useful if you want to store things in a rel database, where arrays are not first choice Throws : If the argument is outside {A,C,G,T} Returns : string Args : character {A,C,G,T}get_arrayTitle : get_array Usage : Function: Returns an array with frequencies for a specified base Returns : array Args : charget_logs_arrayTitle : get_logs_array Usage : Function: Returns an array with log_odds for a specified base Returns : array Args : charidTitle : id Usage : Function: Gets/sets the site id Returns : string Args : stringregexpTitle : regexp Usage : Function: Returns a regular expression which matches the IUPAC convention. N will match X, N, - and . Returns : string Args : none (works at the threshold last used for making the IUPAC string)regexp_arrayTitle : regexp_array Usage : Function: Returns a regular expression which matches the IUPAC convention. N will match X, N, - and . Returns : array Args : none (works at the threshold last used for making the IUPAC string) To do : I have separated regexp and regexp_array, but maybe they can be rewritten as one - just check what should be returned_compress_arrayTitle : _compress_array Usage : Function: Will compress an array of real signed numbers to a string (ie vector of bytes) -127 to +127 for bi-directional(signed) and 0..255 for unsigned Returns : String Args : array reference, followed by an max value and direction (optional, default 1-unsigned),1 unsigned, any other is signed._uncompress_stringTitle : _uncompress_string Usage : Function: Will uncompress a string (vector of bytes) to create an array of real signed numbers (opposite to_compress_array) Returns : string, followed by an max value and direction (optional, default 1-unsigned), 1 unsigned, any other is signed. Args : arrayget_compressed_freqTitle : get_compressed_freq Usage : Function: A method to provide a compressed frequency vector. It uses one byte to code the frequence for one of the probability vectors for one position. Useful for relational database. Improvement of the previous 0..a coding. Example : my $strA=$self->get_compressed_freq('A'); Returns : String Args : charget_compressed_logsTitle : get_compressed_logs Usage : Function: A method to provide a compressed log-odd vector. It uses one byte to code the log value for one of the log-odds vectors for one position. Example : my $strA=$self->get_compressed_logs('A'); Returns : String Args : charsequence_match_weightTitle : sequence_match_weight Usage : Function: This method will calculate the score of a match, based on the PWM if such is associated with the matrix object. Returns undef if no PWM data is available. Throws : if the length of the sequence is different from the matrix width Example : my $score=$matrix->sequence_match_weight('ACGGATAG'); Returns : Floating point Args : stringget_all_vectorsTitle : get_all_vectors Usage : Function: returns all possible sequence vectors to satisfy the PFM under a given threshold Throws : If threshold outside of 0..1 (no sense to do that) Example : my @vectors=$self->get_all_vectors(4); Returns : Array of strings Args : (optional) floating